Once a week during the academic year, an invited speaker (from abroad, as well as from the Czech Republic) talks about his or her scientific work. Colloquium takes
place at the Faculty of Informatics and is open to the scientific community. Lecture dates can be found in the programme.
Tuesday 14.00 - 15.00, D2, FI MU, Botanická 68a

Colloquia programme with abstracts for the Spring 2016 semester

Abstract:
The aim of the talk is to give a reflection on some verification
problems that are famous for not being fully understood so far
and to the research of which the author has also contributed.
This includes the reachability problem for Petri nets, and
especially the equivalence problem for first-order schemes or
deterministic pushdown automata.
The talk will highlight several ideas and structures,
at a rather non-technical level, that have clarified some complicated issues.
These ideas can be viewed as concrete instances of a more general approach to
solving open problems, and the message of the talk thus might become
wider than restricted just to the discussed verification problems.

8. 3. 2016

Dr. Pekka Ruusuvuori, BioMediTech, University of Tampere

Bioimage informatics for prostate cancer research

Abstract:
In this presentation, an overview on image analysis related research
Prostate Cancer Research Center (BioMediTech, University of
Tampere/Tampere University of Technology, Tampere Finland) is given. Our
emphasis is in the analysis of histological images, and we utilize
automated whole slide scanning and stacked sections through the tissue.
We develop methods for quantification of tissue properties from digital
pathology images, with special focus in automated analysis and numerical
description of regions of interest in tissue, and their subsequent
analysis using machine learning. Further, we build 3D models of the
organ through reconstructing from scanned histology slides, preserving
the spatial information in quantitative analysis.

15. 3. 2016

RNDr. Barbora Kozlíková, Ph.D., FI MU

Expressive Visualization of Protein Complexes

Abstract:
Protein–protein docking is attracting increasing attention in drug
discovery research targeting namely interactions between two or more
proteins. Therefore, already several approaches and algorithms for the
computation of these interactions are currently available to the
biochemists. However, each of these algorithms produces many (from dozens
to hundreds) possible solutions, i.e., different spatial conformations of
the interacting proteins. And then it is the task for the domain expert to
explore all solutions and evaluate their biochemical relevance. This task
is very time demanding and requires the visual exploration of individual
solutions. However, the possibilities to visually support this task are
very limited. So in our project we aim to propose several visualization
techniques supporting the exploration process and to link them into a
visual analysis tool which will serve the biochemists as an intuitive
visual interface enhancing their decision process.

Exploring the role of lexico-grammar, multi-word expressions and corrective feedback in vocabulary acquisition

Abstrakt:
The development of English language corpora has allowed us to gain a better understanding of how language actually works. We now fully recognise the importance of word frequency, collocation and word grammar. In the talk Daniel explores possible applications of these insights to mobile learning.

Biography:
Daniel Gorin is the founder of two EdTech companies: phase6 and Alphary. phase6 is a spaced-repetition flashcard system for language learning that was launched in Germany in 2002. It is now used in over 4000 schools with content from all the major German publishers. Alphary goes one step further: it combines the power of artificial intelligence and natural language processing with the latest research on language learning to help users learn English in a more efficient, enjoyable and personalized way. By unlocking the power of the Oxford dictionaries, it aims to be recognized as the smartest app that is available.

5. 4. 2016

doc. Ing. Jiří Sochor, CSc., FI MU

Geometry Analysis of Protein Structures - Ten Years After

Abstract:
10 years after introducing the original method Caver 1.0 several tools and
methods for geometry analysis of protein structures emerged. These methods
gained significant attention in biochemists world and are currently used for
de novo design of enzymes. We will survey the Voronoi approaches originating
from analysis of atom volumes (1974) that evolved in methods for
exploration of protein clefts, pores and cavities. We will describe the
development of CAVER 3.0 and compare it with another solutions. We will give
several examples of methods aiming at tunnels and pores in protein
geometry.

Abstract:
We live immersed in an environment where ICT is all-pervasive, fertilizing and empowering nearly all areas of our life and thus creating interaction and interdependence. This might make it advisable to step back and try to take an unbiased look. We will examine some of the developments, starting with

the state of the industry economically and technologically,

the transition from mM to MtM and its

impacts on us as individual and society.

Additionally we will render tribute to the two anniversaries meriting special attention:

Abstract:
With the advent of smart cell phones and hand-held devices equipped with integrated cameras,
today virtually everyone is a photographer. Every day, we are taking photographs in larger
quantities and often of higher technical qualities than ever before. We share photos,
edit them, search them, archive them, enhance them, capture them for some specific purpose, or
we simply want to make our shots look nice. Current digital cameras do not only capture light,
they in fact compute pictures. There is practically no image that would not be computationally
processed to some extent today. Nevertheless, images taken by amateur photographers often lack
the qualities of professional photos and some image enhancement and/or editing is necessary.
Computational photography evolved from computer graphics, image processing, computer vision,
and optics to solve these issues and to extend the capabilities of current photography and display
technology in general.

In this talk, I will introduce the field of computational photography, its elementary principles
and applications (e.g. extending limited dynamic range, widening field of view, or extending depth of field).
Then, I will focus on our recent work on automatic visual image geo-localization.
Our aim is to accurately find the location and orientation of the camera which captured the image.
We introduce a system for automatic alignment of the query photo with a geo-referenced 3D terrain model.
We propose a new alignment metric to accurately predict the camera orientation succeeding the
large-scale visual localization step. Having a sufficiently accurate match between a photograph
and a 3D model offers new possibilities for image enhancement. It can be used to transform
photographs into a realistic virtual 3D experience, e.g. to automatically highlight elements in the image,
such as the travel path taken, names of mountains, or other landmarks. Furthermore, the synthetic depth map,
and/or the whole 3D model of the queried photo, can be used for novel view synthesis,
image relighting, dehazing or refocusing.

3. 5. 2016

RNDr. Jan Sedmidubský, Ph.D., FI MU

Human Motion Data: Applications, Challenges, and Our Research

Abstract:
The rapid development of motion capturing technologies has caused an
explosion in the usage of human motion data in different fields. For
example, motion data are analyzed in sports to compare performance aspects
of athletes, in security research to identify special-interest persons, in
health care to determine the success of rehabilitative treatments, and in
computer animation to synthesize realistic motions. In the first part of
this presentation, we briefly outline existing motion capturing
technologies utilized in the specific sport, medical and military
applications. We also introduce the main research challenges, mainly from
the perspectives of similarity-based comparison and motion retrieval. In
the second part, we present our novel method for effective comparison of
complex spatio-temporal motion data. We also show a web demo application
for retrieving similar movements in real time.

10. 5. 2016

doc. RNDr. Petr Holub, Ph.D., FI MU

Scalable Storage and Processing of
Privacy-Sensitive Data: More Than Just
a Dream?

Abstract:
Biomedical research is facing tremendous growth of data due to the rapid progression with
analytics technologies. Researchers deal with large data sets of genomics, proteomics, and
metabolomics data, together with imaging exceeding gigapixels per image and large-scale
text mining from the clinical unstructured text records in different languages and information
coding systems. Particular for medical research is dealing with resources coming from individual
persons, whose privacy needs to be protected and who give their consent for sharing
material and data for research purposes. Human-oriented biobanks have become infrastructural
hubs for collecting biological samples and the data, analyzing the samples to generate
additional data, harmonizing the data and sharing it with biomedical researchers. The talk
will address the challenges and possible solutions for storing and processing privacy-sensitive
data in a scalable way, which has turned into major collaboration between biomedical
researchers and computer scientists as well as IT infrastructures.

Abstract:
The latest IT4Innovations computing system - Salomon includes
significant number of many integrated cores architecture. An efficient
use of such architecture needs reviewing of current algorithms and their
adapting for such system. The research team at IT4Innovations is focused
on development of highly scalable algorithms for solution of linear and
non-linear problems by a non-overlapping domain decompositions method
called Finite Element Tearing and Interconnecting method. The most
efficient variants were adapted to the new MIC architecture and
implemented into our in-house software package ESPRESO (ExaScale
PaRallel FETI Solver). Its developers focus on highly efficient
communication layer on top of pure MPI and efficient use of MIC
architectures to improve solvers performance and scalability. Thus
ESPRESO uses three levels of parallelization: 1.) message passing on
node level, 2) threading inside a node using Cilk++ and 3.)
vectorization using Intel MKL library or Cilk++. The experience with
running of ESPRESO solvers on Salomon and other world’s top computing
systems will be presented.